tinyRNA provides an all-in-one solution for precision analysis of sRNA-seq data. At the core of tinyRNA is a highly flexible counting utility, tiny-count, that allows for hierarchical assignment of reads to features based on positional information, extent of feature overlap, 5’ nucleotide, length, and strandedness.
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tiny-count: change selection semantics to broaden scope of hierarchy values #223
Currently, the Hierarchy value (provided via the user's Features Sheet) is used only during Stage 2 selection. Its intended use was to reduce the pool of feature candidates for Stage 3 selection. After further discussion, we've decided that this approach is potentially confusing and that it would make more sense to instead sort feature-rule pairs by their hierarchy value for Stage 3 selection.
Reads assigned to features with a lower hierarchy value will be excluded from features with a higher hierarchy value. Once an alignment has been assigned to a feature-rule pair, the Stage 3 selection process will only continue for other feature-rule pairs of equal hierarchy before returning the selection results.
Currently, the Hierarchy value (provided via the user's Features Sheet) is used only during Stage 2 selection. Its intended use was to reduce the pool of feature candidates for Stage 3 selection. After further discussion, we've decided that this approach is potentially confusing and that it would make more sense to instead sort feature-rule pairs by their hierarchy value for Stage 3 selection.
Reads assigned to features with a lower hierarchy value will be excluded from features with a higher hierarchy value. Once an alignment has been assigned to a feature-rule pair, the Stage 3 selection process will only continue for other feature-rule pairs of equal hierarchy before returning the selection results.